U2AF2 RNA-Seq in K562

General Information


RBP	U2AF2
Cell_Line	K562
Method	shRNA
Exp_Name	U2AF2-BGKLV08-K562
ENCODE_series_ID	ENCSR276OYF
Batch_ID	BGKLV08
Pool ID	Pool-140601
Local_Set_Name	set10
ENCODE_KD_Exp_ID	ENCSR904CJQ
ENCODE_CN_Exp_ID	ENCSR344XID
Rep1	U2AF2-LV08-63
Rep2	U2AF2-LV08-64
CN1	Nontarget-LV08-1_00003531
CN2	nontarget-LV08-2_00003531
Rep1_qPCR	61.0
Rep2_qPCR	65.3
Rep1_WB	80.7
Rep2_WB	85.4
Antibody Cat#	A303-665A
Antibody Lot#	A303-665A
Antibody DCC ID	ENCAB511TCT
Status	Released
Project	ENCODE3
ID	305

Experiment Information (Status: Released)

	BGKLV08-63	BGKLV08-64
idx	68	69
TRCN#_or_BGC#	TRCN0000001162	TRCN0000001162
shRNA_or_gRNA_sequence	CGACGAGGAGTATGAGGAGAT	CGACGAGGAGTATGAGGAGAT
PAM
Name	U2AF2	U2AF2
Sample_ID	BGKLV08-63	BGKLV08-64
transduction_Date	4/4/2014	4/4/2014
days
RBP_name	U2AF2	U2AF2
qPCR_result	61.0	65.3
Ave_qPCR	63.2
RT-qPCR_primer-F	GGCTTGTCAAGTCCATCGAG
RT-qPCR_primer-R	TGGCAGTCAAACACAGAGGT
protein_conc	2877	3335
WB_result	80.7	85.4
Ave_WB	83.0
WB_DONE_date	7/20/2015
MW	54kDa
IP	1	1
antibody_Cat#	A303-665A	A303-665A
Antibody DCC ID	ENCAB511TCT	ENCAB511TCT
submitted_to_DCC_date	8/6/2015
Rep1_TPM	126.407414	0
Rep2_TPM	95.1231617	0
Action	Ready	Ready
Library_start_date	5/9/2014	5/9/2014
repeat_library
Note
ID	73	74

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
U2AF2	Product_ID: A303-665A Lot_ID: 1 Source: Bethyl Labs Target Name: U2AF2-human

Experiment Status

	BGKLV08-63	BGKLV08-64
Sample_ID	BGKLV08-63	BGKLV08-64
Sample Name	U2AF2-LV08-63	U2AF2-LV08-64
Sample Name	U2AF2-LV08-63	U2AF2-LV08-64
RBP	U2AF2	U2AF2
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-09-16	2014-09-16
Project	ENCODE3	ENCODE3
Note
ID	322	323

Library-Prep
Sequencing

Library-Prep Information

	BGKLV08-63	BGKLV08-64
Sample #
Sample Name	U2AF2-BGKLV08-63	U2AF2-BGKLV08-64
Sample_Name_Alias	U2AF2-LV08-63	U2AF2-LV08-64
Index Well Position	S07	S08
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-05-08	2014-05-08
Lib_ID	Lib-140508	Lib-140508
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV08/set5/A2.png	DNA_Library_LV08/set5/B2.png
RIN	9.0	9.2
libSample_RNA_Well	RNA_Library_LV08/set4/A2.png	RNA_Library_LV08/set4/B2.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGKLV08-63	BGKLV08-64
RBP	U2AF2	U2AF2
Batch_ID	BGKLV08	BGKLV08
WB_result	80.700	85.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	1942	1943

Sequencing Information

	BGKLV08-63	BGKLV08-64
Sample_ID	BGKLV08-63	BGKLV08-64
Sample Name	U2AF2-LV08-63	U2AF2-LV08-64
Pool ID	Pool-140601	Pool-140601
LocalServer_folder	set10	set10
total_reads	49,980,000	47,530,000
total_aligned_reads	45,070,790	42,431,092
unique_aligned_reads	41,277,244	38,918,428
percent_uniqueAligned	0.82588	0.81882
correlation_replicates	0.999369	0.999369
spikein_reads	301,754	304,302
percent_spikeins	0.00604	0.00640
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	642	643

Data Submission Information

	BGKLV08-63	BGKLV08-63
ENCODE_alias	brenton-graveley:U2AF2-LV08	brenton-graveley:U2AF2-BGKLV08-K562
ENCODE_accession	ENCSR904CJQ	ENCSR276OYF
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV08-63	BGKLV08-63
Sample Name	U2AF2-LV08-63	U2AF2-LV08-63
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-08-13	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2710	7025

File Information

file_name	file_path	file_format	output_type	assay_type	lab	Sample ID	platform	read_length	run_type	paired_end	assembly	genome_annotation	derived_from	controlled_by	Project	FILE_ID
U2AF2-LV08-63_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	642					GRCh38	V40	U2AF2-LV08-63_CAGATC_L008_R1_001.fastq.gz,U2AF2-LV08-63_CAGATC_L008_R2_001.fastq.gz		ENCORE2	12029
U2AF2-LV08-63_CAGATC_L008_R1_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	642	HiSeq2000	100	paired-ended	1				Nontarget-LV08-1_00003531_GATCAG_L005_R1_001.fastq.gz,nontarget-LV08-2_00003531_TAGCTT_L005_R1_001.fastq.gz	ENCODE3	12085
U2AF2-LV08-63_CAGATC_L008_R2_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	642	HiSeq2000	100	paired-ended	2				Nontarget-LV08-1_00003531_GATCAG_L005_R2_001.fastq.gz,nontarget-LV08-2_00003531_TAGCTT_L005_R2_001.fastq.gz	ENCODE3	12141
U2AF2-LV08-63_Signal.Unique.strand+.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	642					GRCh38	V40	U2AF2-LV08-63/Aligned.sortedByCoord.out.bam		ENCORE2	12197
U2AF2-LV08-63_Signal.Unique.strand-.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	642					GRCh38	V40	U2AF2-LV08-63/Aligned.sortedByCoord.out.bam		ENCORE2	12253
U2AF2-LV08-63_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	642					GRCh38	V40	U2AF2-LV08-63/Aligned.sortedByCoord.out.bam		ENCORE2	12309
U2AF2-LV08-63_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	642					GRCh38	V40	U2AF2-LV08-63/Aligned.sortedByCoord.out.bam		ENCORE2	12365
U2AF2-LV08-63_quant.sf	ENCODE_DATA/set10/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	642					GRCh38	V40	U2AF2-LV08-63_CAGATC_L008_R1_001.fastq.gz,U2AF2-LV08-63_CAGATC_L008_R2_001.fastq.gz		ENCORE2	13364
U2AF2-LV08-64_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	643					GRCh38	V40	U2AF2-LV08-64_ACTTGA_L008_R1_001.fastq.gz,U2AF2-LV08-64_ACTTGA_L008_R2_001.fastq.gz		ENCORE2	12030
U2AF2-LV08-64_ACTTGA_L008_R1_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	643	HiSeq2000	100	paired-ended	1				Nontarget-LV08-1_00003531_GATCAG_L005_R1_001.fastq.gz,nontarget-LV08-2_00003531_TAGCTT_L005_R1_001.fastq.gz	ENCODE3	12086
U2AF2-LV08-64_ACTTGA_L008_R2_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	643	HiSeq2000	100	paired-ended	2				Nontarget-LV08-1_00003531_GATCAG_L005_R2_001.fastq.gz,nontarget-LV08-2_00003531_TAGCTT_L005_R2_001.fastq.gz	ENCODE3	12142
U2AF2-LV08-64_Signal.Unique.strand+.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	643					GRCh38	V40	U2AF2-LV08-64/Aligned.sortedByCoord.out.bam		ENCORE2	12198
U2AF2-LV08-64_Signal.Unique.strand-.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	643					GRCh38	V40	U2AF2-LV08-64/Aligned.sortedByCoord.out.bam		ENCORE2	12254
U2AF2-LV08-64_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	643					GRCh38	V40	U2AF2-LV08-64/Aligned.sortedByCoord.out.bam		ENCORE2	12310
U2AF2-LV08-64_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	643					GRCh38	V40	U2AF2-LV08-64/Aligned.sortedByCoord.out.bam		ENCORE2	12366
U2AF2-LV08-64_quant.sf	ENCODE_DATA/set10/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	643					GRCh38	V40	U2AF2-LV08-64_ACTTGA_L008_R1_001.fastq.gz,U2AF2-LV08-64_ACTTGA_L008_R2_001.fastq.gz		ENCORE2	13365